An Unfinished History
by IzzieStar
Summary: Things have changed in Atlantis, and just as John finds himself contemplating his present, he finds himself unexpectedly reuniting with the past.
1. Chapter 1

**A/N: This is my first fanfic concerning the events after 'Lifeline'. A few things to consider, this fiction doesn't take into account any appearances of Weir after this episode, and I have also changed Sheppard's team slightly for various reasons. Hope you enjoy it!**

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'Okay, tell me this, if there's been this advanced civilization right under our noses all this time, why is there no record of them in the database?' John asked, as he strapped his tactical vest on.

'The Ancients have been gone for a very long time...maybe they, I don't know, developed. This may come as a surprise to you Sheppard but the world wasn't created with computers and cell phones,' Rodney replied.

Choosing not to rise to incredibly tired McKay's bait, Sheppard rolled his eyes at Ronon who was absent-mindedly switching between modes on his gun. They were late. Again. Sheppard was pretty sure that if he had allowed himself to look up to the window of Woolsey's office he'd have been met with yet another look of disappointment. They were becoming a more and more frequent with each mission. It wasn't as if it was even Sheppard fault; Teyla was a Mother now and her priorities lay elsewhere.

'Oh for goodness sake, this is getting ridiculous. I say we just leave without her,' McKay snapped.

'We are not leaving without her.'

'It's not like she really contributes anything anyway.'

At this, Ronon set his gun to 'kill' and raised his eyes to meet Rodney's, who shifted slightly and raised his chin defiantly.

'She's saved your ass on more than one occasion,' Sheppard pointed out.

'Hey! I could have got myself out of there.'

'When I found him, he was screaming like a little girl,' She said, strolling past McKay.

'Cadman,' McKay sighed.

Facing one another, the look of amusement of Laura's face matched by the look of irritation of McKay's, they continued the ongoing battle which felt like it had existed forever. When Teyla had left Atlantis to be a Mother, Laura had felt like the natural option to replace Teyla. That was assuming, of course, that she and Rodney would be able to stop sniping at each for just a single second. They hadn't. Well, barely anyway. It didn't matter what happened on a mission; Cadman saving Rodney's life, Rodney saving Cadman's life, it never stopped. John liked a bit of banter to his team, but this was taking it beyond that. Although, as badly as John was taking it, Woolsey was taking it so much worse. Every debrief was followed by a 'chat', during which the words 'dynamics', 'respect' and 'chemistry' were all mentioned repeatedly and indifferently.

Turning away from Cadman and McKay, John nodded at Ronon and stepped though the now established wormhole. Since they had received the MALP telemetry Rodney had barely been able to contain his excitement at what was 'so obviously' an advanced society and insisted on the team visiting this planet immediately. Their purpose, as pressed by Woolsey, was to establish diplomatic relations, with the possible view of a treaty between the two societies. It had struck Sheppard that, despite Woolsey relevant experience, Woolsey had made the definite decision not to come on this mission, trusting John, the strong and silent Ronon, and the two bickering adults increasingly resembling school children. Probably not Woolsey's wisest decision, John smiled to himself.

'Just look at that,' Rodney said, with uncharacteristic pleasure.

'It's a tall building,' Ronon said, looking at Rodney with confusion.

'It's not just a tall building. Look at the shape...the curvature,' Rodney sighed.

'Geez Rodney, if you like it so much, why don't you just ask it out?' Laura said, with a slight grin.

'What I mean Lieutenant, is that a building like that is a feat of engineering,' Rodney said, icily.

While it may have been a 'feat of engineering', it wasn't exactly the most beautiful building John had ever laid his eyes upon. The base seemed to be formed into the shape of some sort metal donut, while the bulk of the building, which formed a skyscaper overlooking the gate and surrounding landscape, had been built into twist oval shape, made of a grainy-looking metal. As much as Rodney was enjoying the view of the building, John had a feeling the view from the building would be much easier on the eyes, with untouched countryside and trees surrounding them. Actually, now he thought about it, it was actually a rather strange set up...one building and the rest of the countryside untouched? How did they grow food? Where did they all live? While he still wasn't feel the evident excitement of Rodney, his intrigue was certainly piqued.

Approaching the windowless doors to the base, they were stopped in their tracks by the sliding open of the doors to reveal a young woman wearing a burgundy trouser suit, rushing out to meet them. She stopped before them and bowed her head slightly, before looking up at them with the most stunning...purple eyes. Well, that was certainly new. A quick once over confirmed that all apart from her irises were human, but it was still somewhat of a shock.

'You have come to us,' She said, with almost relief in her tone.

'Yes. I'm Colonel Sheppard, this is Lieutenant Cadman, Doctor McKay and Ronon. It's nice to meet you.'

'Welcome. I am Isha. It was you who sent the robot?' She asked.

'Yes. It's actually called a MALP, we use it to check out planets before we come through the gate. You know, check out to make sure there are no big scary monsters,' Rodney said, positively leering.

'The gate. Why we never thought of calling it that. To us, it is the 'entity'. Although I suppose a more accurate description would be the 'unkown entity' I suppose,' Isha said, with a nervous laugh.

'Unknown entity?' Sheppard repeated.

'Why yes. For all our knowledge in our own galaxy, the 'gate' has very much remained an entity for us,' Isha said earnestly.

'Well, perhaps, that might be something we can assist you with,' John said kindly.

'You would help us? Oh! But I am forgetting myself. I must take you to our leader. Come, come,' She said, beckoning the team to follow them into the building.

There were so many questions that John was wanting to ask, and he could practically feel Rodney bursting with them, but he walked in silence, taking in the depressing decor of the building as they were led through corridors and finally into a lift, which was certainly not a regular occurence in the Pegasus Galaxy and only added to his interest. It struck John, as they exited the lift and were led onto yet another corridor, that the inside of the building was much like the outside, with the same grainy metal and soulless feel to it. There were no homely touches; no plants, not paintings, just metal walls, ceilings and floors. At the end of the corridor, they came to a door, still of the same metal, but somehow grander, bigger and more imposing that every other. Something told John they had reached their destination. Isha opened the door slowly, revealing the small room, in the centre of which was control station, so out of place with the other decor of the room. The complicated technology of the control station was placed on a woven rug, surrounded by comfortable chairs and sofa, and in the corner of the room was what John was pretty sure was a liqueur cabinet. Sat behind the control station was man, who John could only assume to be the leader of whom Isha has spoken of. Behind the slightly-crinkled, soft purple eyes, was a strength, a command of respect. He stood up, and walked over to the group shaking his head in smiling amazement.

'We have waited so long,' He said bowing his head, before bringing it up again and smiling.

'Well I'm glad we've ended your wait. I'm Colonel Sheppard and this my team; Mckay, Cadmen and Ronon,' John said awkwardly.

'I am Mande, the leader of this are Pegasusians I am to assume?' He asked warmly.

'Pegasusians? You mean, you're not from this galaxy?' Rodney asked, frowning in confusion.

'We are not. We are explorers from the Merlicia Galaxy.'

Raising his eyebrows slightly in shock, John turned to look at Rodney who he sensed would be handling proceedings for awhile.

'Ha, that's funny because we're in a similar position ourselves. I'm guessing this...building is actually a ship?'

'It is, and I would be honoured to show you the whole of our ship. I sense you are a man of Science, like myself,' Mande said.

'Actually, we were wondering if we could maybe get to know a bit about each other first,' John cut in, before Rodney could agree to another tour. Ship or no ship, it was mundane.

'Of course, you must be tired. Sit, sit.'

The team took seats around the control station, awkwardly looking around the room, as Mande took it upon himself to pour drinks for them all. He then turned, carrying a tray of glasses containing a green substance and offered them each a drink, which John accepted and took a sip from, which he immediately regretted and winced slightly at the bitter taste. Mande took a drink himself which he drank in one swift mouthful, and moved towards a door at the back of the room, which he held open and called 'Teelia'. From the other side of the door, the gentle sound of footsteps could be heard. The first thing he saw was the hair. The brown curly hair. It was longer now. His eyes rose and he met hers. Those green eyes. How they had haunted his dreams.

'Elizabeth,' He let out breathlessly.


	2. Chapter 2

In that split second of silence, it occurred to John just how implausible it was. And yet...she was there. It was her. The hair was longer and she looked relaxed. but it was her. There was no doubt about that. But, how? How could she be here, safe and content, when she should be in Atlantis? John had taken it for granted, without even realising it, that should she escape from the Asurans, she would return to them. She hadn't though and here she was.

It wasn't how he had expected it, if he had expected it at all. He didn't know anymore. She'd been missing for so long that, as much as he couldn't and didn't admit it to himself, Doctor Elizabeth Weir has become the past. Yet, in those moments when he had imagined them reuniting, he'd always assumed he would rescue and save her. He'd vowed he'd find her, and he finally had. It simply didn't fit the picture he had built up in his head.

'Elizabeth,' Elizabeth repeated and bowed her head slightly.

Touching Mande's chest gently with her right hand, Elizabeth brushed passed the man and calmly took the seat across from Sheppard bringing her eyes up to meet his and smiling gently. It unnerved him. He hadn't expected her to fling herself into his, or anybody's, arms, but this placid, calm reaction was equally unexpected. He didn't know what to do or say, and a quick look around his team who were all staring with open mouths, told him that they were experiencing the same confusion.

'My future wife -,' Mande said.

'Wife?' Rodney spat.

'Is this not customary in the Pegasus Galaxy?' Elizabeth asked.

'Well you should know,' Rodney said, his brow furrowing in confusion.

'Then tell me,' Elizabeth laughed.

'What are you doing here?' John asked, his voice betraying the hurt he had been so trying to hide.

'Exploring the Pegasus Galaxy. Well, hoping to,' Elizabeth said, smiling at Mande.

'What I'm trying to say is, why didn't you return to Atlantis?' John asked as gently as he could manage.

'And why couldn't you just dial the gate for them?' Rodney asked, frowning in confusion.

The calm exterior and steady smile dropped from her face and she narrowed her eyes at Sheppard, who, so familiar with the intensity of that gaze, swallowed and looked to his team. Anything not to look at her.

'Perhaps we should - ,' Mande began.

'Atlantis?' Elizabeth asked.

'Of course, after our 'relocation', the gate address changed. Let me guess, you couldn't find us?' Rodney said, with a little more tension in his voice than usual.

'Can we please -,' Mande pleaded with an uncomfortable laugh.

'I'm afraid we haven't been looking for you,' Elizabeth laughed.

'I don't buy that. You might be happy here, now, but you wouldn't turn your back on Atlantis. You believed in our mission,' John said.

'I'm sorry, but I'm afraid I have never turned my back on this Atlantis, because I have never been there.'

John narrowed his eyes at Elizabeth and then he realised, 'Teelia...he called you Teelia.'

'Yes.'

'You are Doctor Elizabeth Weir,' John insisted, firmly.

'I am Teelia, of the Leluvian people,' Elizabeth replied, with equal firmness.

'No you are not,' Rodney said.

Mande let out a nervous laugh, 'If I had known my introducing of Teelia would cause such a fuss, I should never have sought to do so.'

'She is not called Teelia,' Sheppard pressed.

'History that states that is not the case.' Mande said.

'She was our boss for over three years, I am pretty sure I know what I am talking about,' Sheppard said.

'Seriously, what the hell is going on here?' Rodney asked, looking between Elizabeth and Mande.

'It would seem that there is a little confusion on your part,' Elizabeth chuckled.

'Confusion? I don't think so, you may have been missing for a while, but my memory is pretty impressive and you are most definitely Doctor Weir,' Rodney snapped.

'For once, I am actually in agreement with Rodney,' Cadman commented.

'We are from Leluvia in the Merlicia Galaxy. We came here to travel and acquire wider knowledge of the universe, the Ancients,' Elizabeth said passionately.

'That is Elizabeth. That sounds like Elizabeth,' Rodney insisted to Mande.

'I have known Teelia for most of my life,' Manda laughed.

Taking his eyes away from Elizabeth, John discreetly turned his attention to Mande who was watching Elizabeth with a smile. Yet, behind the smile, John sensed there was more; that same determination he had sensed when he first met him, but there was more. There was worry in those eyes. For all his insistence and light tone, his manner suggested that, despite what he was saying, he knew more about 'Teelia' than he was letting on and more even than 'Teelia' knew herself. And they were to be married. He hadn't even allowed himself to consider what that really meant, but what he did know was that Mande wasn't going to let her go, or remember herself, without a fight, and his team simply wasn't ready for that fight yet. Instead, he was going to have to lie. Lie to Mande, lie to his superiors and, worst of all, lie to Elizabeth until he knew he could persuade her of her true identity. To persist would only result in them being pushed out by these people and, therefore risk the possibility never have the chance to see Elizabeth again, he feared.

For a final moment, he studied Elizabeth, looking into those green eyes which looked back, so searchingly into his own and he simply knew, more certain than he had before, that it was her. He could have looked at her for longer, so much longer, but instead he tilted his head down slightly and laughed, an unnatural belly laugh. From the side, he saw his team look at him in confusion and he turned to them continuing the facade.

'This isn't Elizabeth. Elizabeth had brown eyes, Teelia here has green eyes,' John chuckled, widening his eyes at the team.

A slight nod of the head followed by an equally fake laugh from Laura, confirmed to John that she recognised and accepted his silent order, while Ronon...didn't really give much away with his silent stare, but that would do. Rodney on the other hand, simply couldn't accept the prospect of being told he was wrong over something he had such certainty about.

'What? That is Elizabeth. Have you gone mad? Elizabeth had -'

'Atlantis in her heart, so of course she would have returned if she was alive.'

It made no sense, but he had to say something...anything as it turned out, to stop Rodney revealing that he had lied about the eye colour. And from the look of gradual realisation, it had finally hit Rodney what John was trying to achieve with his lie. With his mouth slightly hanging open, in a completely gormless manner, Rodney nodded, before realising himself and closing his mouth before letting out his own fake laugh, causing John to roll his eyes. Yet, Mande was laughing too. And Elizabeth.

Continuing to chuckle, more with relief that genuine amusement John suspected, Mande said, 'Travelling through different galaxies... it is perhaps inevitable that we will come across those who have evolved to look as we do.'

'Well, it's not the first time we've, err, come across doppelgangers during our time in the Pegasus Galaxy,' John said, grimacing slightly.

'We certainly did not expect such a commotion on our first meeting with Pegasusians, did we dear?' Mande asked Elizabeth.

'I have a feeling they might be worth it though,' Elizabeth said smiling at John.


	3. Chapter 3

Once Mande had relaxed again in their company, trusting that they believed they had made an error, John suspected, the excitement that had surrounded their arrival soon returned. The potential for a form of agreement had been suggested tentatively by John, knowing that if they were going to get Elizabeth back, they were going to have to keep Mande on side and have a reason for contact as long as it would take, and Mande had been delighted by the prospect. Briefly, with Mande's obvious willing, John considered the possibility that they may be wrong about Elizabeth after all, but one glance at her ended that possibility in his mind immediately.

Sitting in the same room as her, just metres away from her, a big part of him simply wanted to sit and stare at her, allowing himself to make it real that she was here and to make some logic of something that seemed to illogical. Yet, he could barely look at her. Something was holding him. Actually, he knew very well what was holding him back and it was the exact reason he wanted to look at her. He feared that, in looking at her, he'd give himself, and his team, away. Too much had happened for John to simply sit and look occasionally in Elizabeth's direction as if she was actually 'Teelia' as Mande so clearly wanted, and perhaps needed, for them to do so.

When Mande has accepted their offer of a return visit the following day, John hoped they could make a swift exit, but it was not to be as Mande made his previous offer of a tour around the ship which Rodney accepted before John could, regretfully, pass on the offer. As soon as the words 'engine diagnostics' were mentioned, John decided to make his excuses about needing 'fresh air'. Both Cadman and Ronon swiftly offered to join

him, but only accepted the offer of the latter, telling Cadman he needed her to keep McKay in line. The truth was he couldn't answer the questions she was bursting to ask yet. He needed some time to work it all out in his head, before he was asked for answers he didn't have. Parting from the other half of the team, John and Ronon retraced their steps through the ship in complete silence, which is just what he needed and was why he'd allowed Ronon to join him. In a way, he liked the company; it made him feel calmer somehow. Once they were outside, they strolled towards the gate and paced for awhile before coming together and standing still in silence, looking at the ship before them.

'So you think it's Doctor Weir?' Ronon asked.

'Yeah, I do,' Sheppard confirmed.

And that was all they said on the matter. It was all that could be said for the timing being anyway. Sighing with irritation at Rodney, John looked down at his watch to establish just how long Rodney had been keeping him before. When he looked up again, he was met with the sight of a familiar figure approaching him, and the person wasn't a member of his team. It was Elizabeth. A gentle pang of hope hit his chest as he wondered why she was coming, why she was seeking him out. He found that he suddenly didn't know what to do with himself. Standing still felt awkward and stilted, so he walked towards her with Ronon following him a pace behind.

'Hello again,' Elizabeth said, as she reached him.

'Hey,' John said gently.

'Err; I think I'm going to take a walk,' Ronon commented before turning and walking towards the forest in the distance.

In a way, it was a relief, but it left John feeling terribly exposed. He had no idea what to say, but thankfully Elizabeth was still as eloquent as she ever had been.

'What you said, although slightly frightening for a moment there, it intrigued me. I sense there's a story about this Doctor Elizabeth Weir that is worth a listen. We did come here to learn after all,' Elizabeth said smiling.

With that, all his hopes that she had remembered were destroyed, but he couldn't deny that he was pleased that she had sought him out and was seemingly interested in getting to know something of him, or at least her own history without realising it.

'It's pretty complicated,' John admitted.

'Complicated tends makes the best stories,' Elizabeth commented.

'Well I can't deny that,' John smiled.

'I make you nervous,' Elizabeth commented.

John sighed and looked at her, her face which was so familiar yet so unaware, 'You remind me of her, and, well, I never expected to see her again. It's a bit of a shock.'

Elizabeth nodded, 'She was your boss?'

'Yes, for three years. She led an expedition, a lot like yours, to come the Pegasus Galaxy, to find Atlantis. It was never easy, but she was happy I think. We all were. We were a team...a family even,' Sheppard said, uncomfortably.

'And she went missing?'

'Yes...well, actually no. We left her behind on a mission. She ordered us to leave, but I've never forgiven myself, never stopped wanting to find her again.'

It occurred to John that had she known her true identity, he would never have revealed these feelings to her. He'd never revealed them to anybody and had never really planned to, although, he had a feeling that those closest to him suspected.

'Were you...romantically involved?' Elizabeth asked tentatively.

'No. Just friends and colleagues,' John smiled.

'But you wanted to be more?' Elizabeth continued.

'I've never really thought about it.'

'Haven't you?'

'Even if we had wanted something to happen, our superiors would never have allowed it,' John said, trying to ignore the slight burn in his cheeks.

'I am taking that as a diplomatic 'yes',' Elizabeth said, raising her eyebrow slightly at him.

'It was never that simple. I don't even know if it was a 'yes',' John said, smiling.

Elizabeth nodded, reflecting his smile, but he had a feeling that she didn't believe him and that nothing he could say could make her believe him. In the midst of lies he had to weave though, it was one of the few truths. It had never been that simple with Elizabeth and, to this day, he still didn't know how he really felt for her. There had been moments when he had considered that there might be something more between them, but these moments had been so inconsistent in his mind that he simply couldn't settle on a 'yes' or a 'no'. Yet, here he was telling the woman herself. Although he knew it was Elizabeth, and hoped that she would soon, telling her these things as 'Teelia' felt...easy. He was speaking with an openness which was so unlike him. It had become routine to hide his true feelings, to protect those around him. They looked up to him, and trusted him, and to admit his shortcomings or weaknesses would have felt like a failure on his part.

'I'm sorry that you lost her,' Elizabeth said.

'Yeah, me too, but I've not given up hope yet,' He said, looking into her eyes.

Tentatively, she reached out and gently stroked his cheek with her thumb, in such an uncharacteristic move for the Elizabeth he knew. Despite this, he couldn't deny to himself, that a little part of him enjoyed it, welcomed it even, but then he remembered that this was Elizabeth and that she was comforting his deception. He had his reasons, but that didn't exempt him from feeling the guilt that was niggling away at him. Slowly he reached, up to her hand and took it in his own to bring it away from his cheek, as much as part of him didn't want to. A slightly blush rising to her cheeks, Elizabeth stepped back and looked away from him.

'Sorry, I just -'

They were interrupted by Mande bellowing 'hello' to them, with a slight hint of panic in his eyes as he marched over to them with Rodney and Cadman in tow. The second he was in touching distance, he defensively reached out to bring his arm around Elizabeth's shoulders. In a way, John felt like he had been saved from giving an explanation that he simply didn't have for Elizabeth, although the look of embarrassment in her eyes left his persisting guilt niggling away. He didn't want her to be embarrassed around him; she had no reason to be. He was the one with cause to be embarrassed by his actions.

'You will return tomorrow?' Mande asked hopefully.

'Tomorrow,' John confirmed.

From the corner of his eye, John saw Rodney move to dial the gate, but quickly slipped in front of him, and dialled in the sequence of numbers. He silently hoped Rodney would not make comment, which he thankfully had the tact not to, as John walked past him to the gate.

'It's fascinating,' Mande commented.

'Well tomorrow you can start using it for yourself,' Laura said, with a smile.

'I would ask if we could join you, but I know you will have much to discuss with your leader,' Mande said.

John nodded at both Mande and Elizabeth, who smiled at him, before turning his back on them and following his team through the gate. When he reached the other side, he was met with three accusatory pairs of eyes.

'Atlantis has sure changed,' Laura said.


End file.
